Since NCBI is pretty unreliable for large downloads using fasterq-dump then we should look at alternatives.
Once we know the SRR number then we can fairly easily get the data from ENA using:
https://www.ebi.ac.uk/ena/portal/api/filereport?accession=SRR11189100&result=read_run&fields=run_accession,fastq_ftp
which gives us something like:
run_accession fastq_ftp
SRR11189100 ftp.sra.ebi.ac.uk/vol1/fastq/SRR111/000/SRR11189100/SRR11189100_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR111/000/SRR11189100/SRR11189100_2.fastq.gz
..which we can then download with either FTP or HTTP, and it comes down already compressed which is a bonus. We could easily have multiple back ends for the download and try all of them if a sample is being a pain.
Since NCBI is pretty unreliable for large downloads using fasterq-dump then we should look at alternatives.
Once we know the SRR number then we can fairly easily get the data from ENA using:
which gives us something like:
..which we can then download with either FTP or HTTP, and it comes down already compressed which is a bonus. We could easily have multiple back ends for the download and try all of them if a sample is being a pain.